CN104115190B - For subtracting the method and system of background in the picture - Google Patents
For subtracting the method and system of background in the picture Download PDFInfo
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- CN104115190B CN104115190B CN201280058524.5A CN201280058524A CN104115190B CN 104115190 B CN104115190 B CN 104115190B CN 201280058524 A CN201280058524 A CN 201280058524A CN 104115190 B CN104115190 B CN 104115190B
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- base portion
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- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
- G06T7/00—Image analysis
- G06T7/0002—Inspection of images, e.g. flaw detection
- G06T7/0012—Biomedical image inspection
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
- G06T5/00—Image enhancement or restoration
- G06T5/50—Image enhancement or restoration by the use of more than one image, e.g. averaging, subtraction
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
- G06T7/00—Image analysis
- G06T7/70—Determining position or orientation of objects or cameras
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
- G06T2207/00—Indexing scheme for image analysis or image enhancement
- G06T2207/20—Special algorithmic details
- G06T2207/20068—Projection on vertical or horizontal image axis
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
- G06T2207/00—Indexing scheme for image analysis or image enhancement
- G06T2207/30—Subject of image; Context of image processing
- G06T2207/30004—Biomedical image processing
- G06T2207/30024—Cell structures in vitro; Tissue sections in vitro
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
- G06T2207/00—Indexing scheme for image analysis or image enhancement
- G06T2207/30—Subject of image; Context of image processing
- G06T2207/30004—Biomedical image processing
- G06T2207/30072—Microarray; Biochip, DNA array; Well plate
Abstract
The present invention provides for improving the method for picture quality.This method includes the image data for receiving substrate, and wherein image data is by generating substrate imaging, and image is generated from image data.This method further includes from the background noise portions generation background of image and represents that wherein background parts include further handling undesirable signal message；And represented by subtracting background from image, generation subtracts the image of background.In this way, individual background image is not required to improve picture quality to subtract background from the image including region-of-interest.
Description
Cross reference to related applications
This application claims No. 61/541,453 U.S. Provisional Application submitted for 30th in September in 2011, in September, 2011
No. 61/541,515 U.S. Provisional Application submitted for 30th and No. 61/660,343 submitted on June 15th, 2012
The rights and interests of the priority of U.S. Provisional Application, the full content of all above applications are incorporated herein by reference.
Background technology
Have been used to monitor, measure, and/or analyze in real time these instead for the optical system of biology and biochemical reaction
It should.This system chemically reacts commonly used in sequence, Genotyping, PCR (PCR) and other biological, with
Monitoring progress simultaneously provides quantized data.For example, optical excitation beam can be used for irradiating hybridization probe in real-time PCR (qPCR) reactions
Or molecular beacon, to provide the fluorescence signal of the amount of instruction target gene or other nucleotide sequences.Test or experiment carry every time
The instrument that can be carried out at the same time more than ever before quantitative response is caused for the increasing demand of larger number reaction.
The increase that sample reaction is counted out in test or experiment has caused to provide the droplet than previous smaller sample volume
Fixed board and other sample patterns.In addition, the technology of such as digital pcr (dPCR) has increased the demand of more small sample volumes, wherein
The more small sample volumes include the Target Nucleotide Sequence of zero or positive number in all test samples.
In addition, in general, in order to improve efficiency, automated system is had increasing need for.For example, automatic biological sample process instrument
The progress of device allow to sample carry out faster, more efficient and high-throughput analysis.The systems of these types is than previous
Greater number of sample is determined in unified test.Therefore, the sample of each measure is subjected to using identifier marking or is marked.
In the past, the operator of system or instrument was possible must be by reading sample acquiring device, rack or measuring on chip
Identifier manually track or verify sample.This kind tracking or verification may be labor-intensive and with high behaviour manually
It slips up (such as sample error tracking or unsuitable test) probability.It will be more more additionally, it is desirable to which measured number of samples is more
It takes and troublesome.
Other systems more automated can scan identifier before testing, to track or verify sample.However, these systems
It is generally necessary to additional component.In addition, identifier may be misread by system or cannot be read by system.
Therefore, because the system of higher throughput is detected and analyzed a large amount of corpusculum product samples, when volume becomes more
Hour, the cumulative effect of system background noise becomes more and more important, removes due to undesirable transmitting or physics work in system
Background noise caused by part becomes more and more important so as to carrying out accurately analysis.
In the past, image is so handled, i.e., is imaged first background substrate, to generate data, then the data can be used for
It is reduced in the image data generated from the substrate imaging for making to include region-of-interest.
The content of the invention
In an illustrative embodiments, provide to improve the method for picture quality.This method includes receiving base
The image data at bottom, the wherein image data are by generating substrate imaging, and image is generated from the image data.The party
Method is further included to be represented from the background noise portions of image generation background, and wherein the background parts include further processing institute not phase
The signal message of prestige and represent that generation subtracts the image of background by subtracting background from image.It in this way, need not be single
Only background image improves picture quality to subtract background from the image including region-of-interest.
Description of the drawings
Fig. 1 is the block diagram for the computer system for showing the embodiment that can implement this introduction；
Fig. 2 is the block diagram of PCR (PCR) instrument for showing the embodiment that can implement this introduction；
Fig. 3 shows the sample chip according to each embodiment described herein；
Fig. 4 shows the exemplary input image according to each embodiment described herein；
Fig. 5 shows the example projected according to the row of the input picture of each embodiment described herein；
Fig. 6 is the flow chart for showing the illustrative methods according to each embodiment described herein；
Fig. 7 A show the example projected according to the row of the input picture of each embodiment described herein；
Fig. 7 B show the example of the base portion baseline projected according to the row of Fig. 7 A of each embodiment described herein；
Fig. 7 C are shown to be projected according to the exemplary row of Fig. 6 A for eliminating base portion of each embodiment described herein；
Fig. 7 D show the mark for projecting and determining according to the exemplary row of Fig. 6 A of each embodiment described herein；
Fig. 8 is the flow chart for showing the illustrative methods according to each embodiment described herein；
Fig. 9 shows the another exemplary input picture according to each embodiment described herein；
Figure 10 A show to be arranged according to the another exemplary of each embodiment described herein and project；
Figure 10 B are shown to be thrown according to the exemplary row of Figure 10 A for eliminating base portion of each embodiment described herein
Shadow；
Figure 10 C show what is determined according to the exemplary row projection based on Figure 10 A of each embodiment described herein
Row mark；
Figure 11 shows the exemplary compartment wall grid image according to each embodiment described herein；
Figure 12 is shown according to the projection of the exemplary row of each embodiment described herein, threshold value and definite sample
This hole；
Figure 13 is the exemplary side being used for from image removal base portion shown according to each embodiment described herein
The flow chart of method；
Figure 14 shows the example images according to each embodiment described herein；
Figure 15 A show the exemplary of the base portion that is determined according to the image of slave Figure 14 of each embodiment described herein
It represents；
Figure 15 B show the another of the base portion shown in Figure 15 A of the interpolative data of the spaced walls including being used between subarray
One exemplary representation；
Figure 15 C show the another of base portion shown in Figure 15 B of the data for being smoothed in the whole surface for be included in substrate
Exemplary representation；And
Figure 16 shows the exemplary processed image for eliminating base portion according to each embodiment described herein.
Specific embodiment
Exemplary system with each relevant method of embodiment described herein including being described in following application
System：No. 61/541,453 U.S. Provisional Patent Application No. (file number：LT00578PRO), No. 61/541,515 U.S. is interim
Patent application (file number：LT00578PRO3), No. 61/541,342 U.S. Provisional Patent Application (file number：
LT00581PRO), No. 29/403,049 U.S. Provisional Patent Application (file number：LT00582DES), No. 61/541,495
U.S. Provisional Patent Application (file number：LT00583PRO), No. 61/541,366 U.S. Provisional Patent Application (file number：
) and No. 61/541,371 U.S. Provisional Patent Application (file number LT00584.1PRO：LT00594PRO), it is all of above
Application was all submitted on the 30th in September in 2011, and all of above application is all totally integrating herein by quoting.With this paper
Described in the exemplary system of the relevant method of each embodiment be included in No. 61/660,569 U.S. Provisional Patent Application
(file number：) and No. 61/660,343 U.S. Provisional Patent Application (file number LT00702PRO：LT00702PRO2 described in)
System, apply all submitting on June 15th, 2012 above, and the full content applied above is incorporated by reference into this
Text.
For a more complete understanding of the present invention, a large amount of details are described below, such as concrete configuration, parameter, example.
It however, it should be understood that the scope that these descriptions are not intended to limit the invention, but for preferably describing exemplary embodiment party
Formula.
Embodiment there is provided the references determined in automated system in sample substrate according to described herein respectively
Point.Specifically, it is determined by the reference point of substrate in the image of automated system acquisition.In general, without such as in sample substrate
Datum mark mark in semiconductor manufacturing.In addition, when making there is the substrate of multiple reflecting points to be imaged, there may be suitable big figure
Optical scattering noise and optical heterogeneity.Despite the presence of these obstacles, each embodiment according to this teaching still can determine
Reference point.
In order to perform other algorithms (such as machine reads the part of image, to identify such as substrate), system may need to have
There is the mark position in substrate, with start to process.
In addition, according to each embodiment, substrate can be detected in automated system.The appropriate installation or positioning of substrate
It can be determined together with the width of substrate.
Therefore, according to each embodiment, it can detect the substrate for including multiple reflecting points and can determine reference point.At one
In example, multiple reflecting points can be grouped into subarray on the metallic substrate.In identical example, larger portion of metal can divide
From adjacent subarray.To have known geometry and size using the substrate in automated system.Geometry and
Size is storable in the memory of system.
Moreover, according to respectively embodiment there is provided for determining the system of the reference point of substrate and quick figure in the picture
As processing method.In addition, embodiment described herein can be implemented according to all optical distortion patterns.
In some cases, above-mentioned calibration method may be enough to carry out desired analysis using bio-instruments.At other
In the case of, more methods can be used for obtaining the transmitting data that preferably data of Indicator Reaction point position and removal detect
In distortion and other undesirable background noises.For example, some background noises in data may be due to the object in substrate
The housing of substrate is kept in reason source and instrument, such as dust granule or cut.Other background noises in data may be due to coming
Natural radiation from instrument surface, such as reflection and natural fluorescence.For example, other background noises may also emit data by detection
Optical system or light source cause.According to the embodiment of the present invention, the expression of background noise can be referred to base portion
(pedestal), background or needle position misalignment.For example, it obtains from operation data, calibration data or during instrumentation
Data determine background.
Biosystem can detect hundreds of to thousands of a samples, and all these samples may be very small volume, such as small
In one nanoliter.Therefore, according to each embodiment, other background noise minimizing technologies can be used alone or with school described herein
Quasi- method is applied in combination, so as to determining and analyzing the transmitting data from sample volume.In some embodiments, sample body
Long-pending position can more accurately determine in substrate, more accurately be analyzed with performing.For example, in some cases, such as digital pcr
Analysis, can more accurately distinguish between non-reaction and the reaction in volume can generate more accurately result.In addition, according to retouching herein
Each embodiment stated, empty reflecting point can be distinguished with the sample volume in the reflecting point without reaction, and without reaction
Reflecting point in sample volume can also be distinguished with the sample volume in the hole reacted or through hole.For example, according to this religion
Each embodiment in leading, reflecting point can be hole, point, recess or through hole.
According to each embodiment described herein, background noise removal may include analysis of image data and processing.The party
Method may include the intensity value for analyzing image data, and interpolation can be carried out from the background noise that the image of substrate removes with to.With this
Mode may further determine that the position in sample volume image.
Computer-implemented system
It would be recognized by those skilled in the art that hardware, software, firmware or its combination can be used in the operation of each embodiment
(depend on the circumstances) implements.For example, its under some handle usable processor or software, firmware or firmware hardwired logic controls
His digital circuit performs.(term " logic " being able to carry out of in this article referring to arrive as recognized by those skilled in the art
The fixed hardware of above-mentioned function, programmable logic and/or its appropriate combination).Software and firmware are storable in non-transient meter
On calculation machine readable medium.Analog circuit can be used to realize in some other processes, this is for those of ordinary skills
It is well-known.In addition, memory or other storage devices and communication component can be used on embodiments of the present invention
In.
Fig. 1 is the block diagram that can be used for performing the computer system 100 of processing function shown according to each embodiment.It holds
The instrument of row experiment can be connected with exemplary computer system 100.According to each embodiment, the instrument that may be used is the heat of Fig. 2
The thermal cycler system 300 of circulating instrument system 200 or Fig. 3.Computing system 100 may include one or more processors (as handled
Device 104).For example, universal or special processing engine can be used in processor 104, (such as microprocessor, controller or other controls are patrolled
Volume) implement.In this example, processor 104 is connected with bus 102 or other communication medias.
In addition, it will be appreciated that the computing system 100 of Fig. 1 can be implemented in any form, it such as can for given application or environment
Can be desired or appropriate frame type computer, large scale computer, supercomputer, server, client computer, desktop computer, pen
Remember this computer, tablet computer, Handheld computing device (for example, PDA, cellular phone, smart phone, palm PC etc.), collect
The special or universal computing device of group's grid (cluster grid), net book, embedded system or any other type).Separately
Outside, computing system 100 may include conventional network system or integrated with LIS/LIMS facilities, and wherein conventional network system includes visitor
Family machine/server environment and one or more database servers.A large amount of conventional network systems are known in the art, including
LAN (LAN) or wide area network (WAN), and including wireless and/or wired component.In addition, client/server environment, number
It is well documented according to storehouse server and network in this field.According to each embodiment described herein, computing system 200 can match somebody with somebody
It is set to and is connected with one or more of distributed network server.Computing system 200 can from distributed network receive information or
Update.Computing system 200 can also transmit the information that will be stored in distributed network, which can be by being connected with distributed network
Other client computer access.
Computing system 100 may include bus 102 or other communication agencies for transmitting information, and processor 104 with
Bus 102 couples to handle information.
Computing system 100 further includes the memory coupled with bus 102 for storing the instruction that will be performed by processor 104
106, which can be random access storage device (RAM) or other dynamic memories.Memory 106 can also be used to perform
Temporary variable or other average informations are stored during the instruction that will be performed by processor 104.Computing system 100 further includes and bus
102 connections set for storing the read-only memory (ROM) 108 of the static information of processor 104 and instruction or other static storages
It is standby.
Computing system 100 may also include storage device 110, such as disk, CD or solid state drive (SSD), be provided
Bus 102 is coupled to for storing information and instruction.Storage device 110 may include that media drive and removable Storage connect
Mouthful.Media drive may include the driver or other mechanisms of supporting fixed or moveable storage medium, such as hard drive
Device, floppy disk, tape drive, CD drive, CD or DVD drive (R or RW), flash disc drives or other are removable
Dynamic or fixed media drive.As illustrated by these examples, storage medium may include computer readable storage medium, the storage
Specific computer software, instruction or data are stored in medium.
In substitutability embodiment, storage device 110 may include other similar media for allowing computer journey
Sequence or other instructions or data are loaded into computing system 100.This medium may include for example to allow by software and data from depositing
Storage equipment 110 is sent to the removable memory module and interface of computer system 100, as program cartridge and boxlike store
Device interface, removable memory (for example, flash memory or other removable Storage modules) and memory bank and other
Removable memory module and interface.
Computing system 100 may also include communication interface 118.Communication interface 118 can be used for software and data is allowed to calculate
It is transmitted between system 100 and external equipment.The example of communication interface 118 may include modem, network interface (such as Ethernet
Or other NIC cards), communication port (for example, USB port, RS-232C serial ports), PCMCIA slot and pcmcia card, bluetooth
Deng.The software and data transmitted by communication interface 118 can be can be received by communication interface 118 it is electronics, electromagnetism,
Optical and other signals forms.These signals can pass through such as wireless medium, conducting wire or cable, light by communication interface 118
Fine or other communication medias passages send and receive.Some examples of passage include telephone wire, cellular phone link, RF chains
Road, network interface, LAN or wide area network and other communication ports.
Computing system 100 can be attached to display 112 (such as cathode-ray tube (CRT) or liquid crystal display by bus 102
(LCD)), wherein display 112 is used to show information for computer user.E.g., including alphanumeric key and other keys is defeated
Enter equipment 114 with bus 102 to couple, to transfer information and command selection for processor 104.Input equipment, which can also be, to be configured with
The display (such as LCD display) of touch screen input ability.Another user input equipment is cursor control device 116, is such as used
In mouse, rail for 104 direction of transfer information of processor and command selection and for cursor to be controlled to move on the display 112
Mark ball or cursor direction key.The input equipment usually has two degree of freedom (first axle (for example, x) on two axis
With second axis (for example, y)) so as to allowing the position in equipment given side.Computing system 100 provides data processing and provides and is somebody's turn to do
The confidence level of data.What some implementations with the embodiment of this introduction met, data processing and confidence level are by computing system
100 provide the one or more sequences for being performed with answer processor 104 and being included in the instruction of one or more of memory 106.
The instruction can be from another computer-readable medium (such as storage device 110) read in memory 106.It performs and is included in memory
Command sequence in 106 causes processor 104 to perform process described herein.Alternately, hard-wired circuit can be used for generation
It is combined for software instruction or with software instruction, to implement the embodiment of this introduction.Therefore the implementation of the embodiment of this introduction
It is not limited to any specific combination of hardware circuit and software.
Term " computer-readable medium " used herein and " computer program product " typically refer to be related to processing
Device 104 provides one or more sequences for execution or any medium of one or more instructions.When implemented, usually claimed
Make meter for the instruction (its can in the form of a computer program or the grouping of forms of other groupings) of " computer program code "
Calculation system 100 is able to carry out the feature and function of embodiments of the present invention.Non-transient computer-readable media these and its
His form may include but be not limited to non-volatile media, Volatile media and transmission medium.Non-volatile media includes for example solid
State disk, CD or disk, such as storage device 110.Volatile media includes dynamic memory, such as memory 106.Transmission medium bag
Coaxial cable, copper wire and optical fiber are included, the electric wire including including bus 102.
The common form of computer-readable medium includes such as floppy disk (floppy disk), floppy disk (flexible
Disk), hard disk, tape or any other magnetic medium, CD-ROM, any other optical medium, punched card, paper tape, Ren Heqi
He has physical medium, RAM, PROM and EPROM, FLASH-EPROM or any other memory chip or box of sectional hole patterns
Formula memory, carrier wave as described below or any other computer-readable medium.
Various forms of computer-readable mediums can relate to transport to processor 104 and be instructed for the one or more of execution
One or more sequences.For example, the instruction is initially carried on the disk of remote computer.Remote computer can refer to this
Order is loaded into its dynamic memory and sends the instruction by telephone line using modem.The sheet of computing system 100
Ground modem can receive the data on telephone line and convert a signal into infrared signal using infrared transmitter.With bus
The infrared detector of 102 connections can receive the data carried in infrared signal and the data are placed in bus 102.Bus
The data are transported to memory 106 by 102, and processor 104 obtains from memory 106 and instructs and execute instruction.By memory 106
The instruction of reception is optionally stored in before being performed by processor 104 or after performing in storage device 110.
It should be appreciated that for the sake of clarity, above description is with reference to different functional unit and processor to the present invention
Embodiment be described.It will be apparent, however, that appointing between different functional units, processor or domain can be used
What suitable function distribution is without departing from the present invention.For example, above-mentioned will be by the function of individual processor or controller execution
It can be performed by same processor or controller.Therefore, should be only considered as with reference to specific functional unit with reference to suitable device, to carry
For the stringent logic of described function rather than instruction or physical arrangement or tissue.
PCR instrument
As described above, the instrument according to workable for each embodiment is (but not limited to) PCR (PCR) instrument
Device.Fig. 2 is the block diagram for showing to implement the exemplary instrument of the embodiment of this introduction.PCR instrument 200 may include to be placed on more
The hot covering 210 of a 212 top of sample, the plurality of sample 212 are included in sample support apparatus (not shown).In each implementation
In mode, sample support apparatus can be the sheet glass or plastic sheet for having multiple reflecting points, and reflecting point is in itself and hot covering
There is covering between 210.Some examples of sample support apparatus may include (but not limited to) porous plate, and (such as standard is micro
Titrate 96 orifice plates, 384 orifice plates) or miniature cards or substantially flat supporting member (such as sheet glass or plastic sheet).Sample support apparatus
Each embodiment in reflecting point may include to be formed rule on the surface of the substrate or irregular array patterning depression,
Recess, ridge projections, and combinations thereof.Reflecting point may be additionally referred to as region-of-interest.Each embodiment of PCR instrument includes sample block
214th, element 216, heat exchanger 218, control system 220 and the user interface 222 for heating and cooling down.According to this teaching
Each embodiment of heat block component includes the component 214-218 of PCR instrument 200 in Fig. 2.
Real-time PCR instrument 200 has optical system 224.In fig. 2, optical system 224 can have the photograph of transmitting electromagnetic energy
Source (not shown), optical sensor, detector or imager (not shown) are penetrated, for from the sample 212 in sample support apparatus
Receive electromagnetic energy and the optical device 240 for electromagnetic energy to be directed to imager from each DNA sample.According to each embodiment party
Formula, optical system 224 can be CCD camera or fluorescence camera.
For the embodiment of PCR instrument in Fig. 2 200, control system 220 can be used for control detecting system, hot covering,
And the function of heat block component.Control system 220 can be by the user interface 222 of the PCR instrument 200 in Fig. 2 by terminal user
It accesses.In addition, computer system 100 as shown in Figure 1 can be used for the control function and the user that provide the PCR instrument 200 of Fig. 2
Interface function.In addition, the computer system 100 of Fig. 1 can provide data processing, display and report preparatory function.All these instrument
Device control function, which can locally be exclusively used in PCR instrument or the computer system 100 of Fig. 1, can be provided to will beg in more detail below
The all or part of remote control of the control of opinion, analysis and function of reporting.
For the purpose of illustration and description, provide this introduction respectively implement be described below.The description is not detailed
And this introduction is not made to be limited to disclosed concrete form.According to the above instruction, it can modify and modification or can pass through
This introduction is realized to obtain modifications and variations.In addition, described implementation includes software, but this introduction can be embodied as hardware with
The combination of software or only with hardware realization.This introduction can utilize object-oriented and not face object programing system to implement.
Other systems and application
In various embodiments, equipment described herein, instrument, system and method can be used for detection is one or more to close
The biotic component of note.Biotic components of these concerns can be any suitable biological targets, which includes but unlimited
In DNA sequence dna (including Cell-free DNA), RNA sequence, gene, oligonucleotides, molecule, protein, biomarker, cell (example
Such as, circulating tumor cell) or any other suitable target biological molecules.
In various embodiments, which can be in the application with various PCR, qPCR and/or dPCR methods and being
System is used in combination, these applications e.g. fetal diagnosis, multiple dPCR, viral diagnosis and quantitative criteria, Genotyping, sequencing are tested
Card, abrupt climatic change, genetically modified organism detection, Rare allele detection and copy number variation.Embodiment of the present disclosure is usual
It is related to the equipment, instrument, the system and method that monitor or measure the biological respinse of a large amount of corpusculum product samples.For example, as herein
Used in, sample can be described as sample volume or reaction volume.
Although being commonly available to the quantitative polyase chain reaction (qPCR) of processing great amount of samples, but it should be appreciated that according to
Each embodiment described herein can use any suitable PCR method.For example, suitable PCR method include it is (but unlimited
In) digital pcr, ApoE gene, asymmetric PCR, ligation-mediated PCR, multiplex PCR, nest-type PRC, qPCR, gene
Group step is moved and bridge-type PCR.
As described below, for example, according to each embodiment described herein, reflecting point may include (but not limited to) through hole,
Hole, recess, point, chamber, sample-holding region, reflecting point and reative cell.
In addition, as used herein, thermal cycle may include for example using thermal cycler, isothermal duplication, and thermal convection current is red
Outer mediation thermal cycle or the enzymatic amplification that untwists.In some embodiments, chip can be integrated with built-in heating element.
For example, according to each embodiment, target detection can be (but being not limited to) fluoroscopic examination, positive or negative ion detection,
PH value detection, voltage detecting or current detecting or its combination.
Fig. 3 shows the substrate 300 there are two identifier according to the mark of each embodiment.Multiple samples may include for
In the reflecting point area 302 tested in a substrate 300.Reflecting point area 302 is shown as array.In other examples, instead
Ying Dian areas may include a sample.In some embodiments, multiple substrates 300 can be located in the system for test.Example
Such as, two, four or 20 substrates 300 can be placed in the instrument system for test.In some embodiments, survey
Determine ingredient and can also pre-install together with sample to be loaded onto in reflecting point area 302.Reflecting point area 302 includes multiple subarrays.In subarray
Between, spaced walls (such as spaced walls 308 and spaced walls 310) can separate subarray.Each subarray may include multiple individual
Reflecting point, such as hole.In this example, substrate has the predetermined pattern of the subarray of reflecting point.It will be appreciated that reflecting point can be with it
He is arranged pattern.Embodiment described herein uses the predetermined pattern or arrangement of reflecting point.
Machine readable identifier in embodiment shown in Fig. 3 is bar code 304 and alphanumeric code 306.
It should be recognized, however, that according to embodiment described herein, machine readable identifier can be such as bar code, text
Originally, number or other symbols and any combination thereof.It can as described above, finding reference point according to embodiment described herein
It can be reading or detect the factor in the other methods of these identifiers.
Fig. 4 shows the exemplary input image of four sample substrates 402,404,406 and 408.It, should according to each embodiment
Image can be reflected light image or fluoroscopic image.In general, each the image data at base center is than the image of edge
The quality of data is good.There may be low contrasts and high contrast or abnormal for perimeter in substrate and the perimeter in image
Become.Therefore according to each embodiment, determine that position of the substrate in image is useful.
Fig. 5 shows the row projection of the example images shown in Fig. 4.Y-axis represents gray level measured value.According to each implementation
Mode, projection refer to the sum along all pixels gray-scale value to boning out.That is, each column pixel is accumulated using path
Point.Similarly, row projection refers to sum to all pixels of the row along image.According to each embodiment party described herein
Formula, projection for extracting feature in particular directions, to be further analyzed.It will also be recognized that according to each embodiment,
It can be projected on other paths in addition to row and column and dimension, in order to which pattern determines.It for example, can be by two
Projection generation is carried out in dimension can determine the projection on surface from the two-dimensional projection that surface subtracts.In other examples, partly
It, can be in other several dimensions using throwing based on the desired geometry in region for needing base portion removal and/or the pattern of feature
Shadow.
For example, the row projection 510 in Fig. 5 shows the gray scale of path integral or each column pixel in the example images of Fig. 4
The sum of grade.In addition, path integral is standardized as maximum 1000 or other suitable values.
It can determine that four substrates 502,504,506 and 508 occur in the picture from row projection 510.This can be by setting certain
One horizontal threshold value 512 is completed.If row projection 510 passes through threshold value 512, it may be determined that it is the edge of substrate.In addition, example
Such as, if it is known that system should include four substrates, then it can it is expected that row projection 510 will intersect eight times (in four substrates with threshold value 512
Each tool there are two edges).Therefore, in row projection 510, four substrates 502,504,506 and 508 are detected.According to each
Embodiment in this way, can check whether the substrate of desired number in system occur.In the example depicted in fig. 5, it is expected
And detect four sample substrates.In addition, known spacings between multiple substrates can be used for determining distinguishing it is external and/or
The position of the detected substrate of defective object and rational desired size.As described above, it is being differently directed the projection of generation
Data can be used for detection with the substrate being differently directed.
Fig. 6 is the flow for showing the illustrative methods 600 for finding substrate location in the picture according to each embodiment
Figure.In step 602, processor receives the image data of substrate.For example, when substrate is imaged by optical system 224 (Fig. 2),
Image data can be generated.In step 604, processor generates data for projection from image data.It can be by calculating the ash along path
Degree grade measured value and generate data for projection.In step 606, processor assesses projection based on the Given information on substrate
The desired pattern of data, such as mark.In various embodiments, the pattern of mark can be the spaced walls for separating subarray.Because
Spaced walls should separate the pixel (a certain pixel wide) of a certain number, and according to the dimension of substrate, system can be found in desired locations
Next spaced walls simultaneously check the width for being detected spaced walls as needed.Therefore, in step 608, in image, the position of mark
It puts and is determined.
In fig. 7a it is shown that the row projection 700 according to substrate of each embodiment described herein.
Fig. 7 B describe row projection 700 and definite base portion 702.Herein, according to each embodiment, comprising need not
The base portion of information may be unfavorable, and may complicate further processing.Base portion can by optics tonal noise and
Optics inconsistency causes.
According to each embodiment, base portion can be determined by multiple methods.For example, local minimum can be determined in projection, and
And curve can be fitted these minimum values.It can determine to determine the position of local minimum in known base pattern.For example,
With reference to figure 4, it is known that a substrate 402 is by the subarray dimension with 4x12 subarrays.Therefore, it is expert at projection (as shown in Figure 7 B)
It is middle to find pattern corresponding with 12 expectation subarrays.It in addition, can be based on the inspection between minimum value and definite matched curve
It looks into, adjusts matched curve.
As another example that base portion determines, base portion includes the bottom envelope of the projection in addition to the borderline region of estimation.
For example, the border of bottom envelope can be fitted to the polynomial curve of seven order polynomial curves or another desired number of times.Then exist
The minimum value of projection, which is less than at the position of polynomial curve, adjusts polynomial curve to the minimum value of projection, to form new bottom
Portion's envelope.Then the new bottom envelope is fitted to another seven order polynomial.Multinomial coefficient is used for by anti-in substrate
Polynomial value is sought to calculate base portion at all data sample positions between the estimation borderline region that should be put.Borderline region it
Outside, the endpoint value based on polynomial curve fills base portion using constant value, to obtain final base portion baseline.Base portion is by subtracting
Base portion bottom line and be removed, so as to remove base portion from drop shadow curve, and the data outside border are set as zero.
Fig. 7 C show the row projection 700 that base portion 702 is removed.It from row projection 700 by subtracting definite base portion 702
And it is removed.In this way, the noise from optical distortion is weakened and subsequent processing may be simpler.It is for example, logical
Removal base portion is crossed, the appropriate local threshold method for finding spaced walls, other marks or each reflecting point can be used for analyzing image
Data.These methods include but is not limited to Otsu threshold methods, average threshold method and intermediate value threshold method.
Because the pattern of substrate is known, can determine image what is partly corresponding with the desired pattern.
Fig. 8 shows the illustrative methods 800 for being used to determine the mark of substrate according to each embodiment.As previously mentioned, substrate
Central area may have better quality image data.It, can in order to determine all positions for it is expected to indicate (such as spaced walls)
Start to analyze data in desired central area.Central area in data for projection determines in step 802.For the base of substrate
This pattern searches central area, in this case, eight independent reflecting points between two boundary interval walls have phase
Width and higher image pixel value to bigger.The step provide substrate for example each reflecting point of measurement feature spacing and
The spacing in next door.By searching for the left side and right side of desired center, other spaced walls can be positioned.With desired interval
The corresponding pixel quantity of wall wide degree can also be known and be storable in memory.For example, in some embodiments, the phase
The wall bulkhead width of prestige can be 20 pixels.
In step 804 and 806, the left side of central area and the region on right side are checked for other spaced walls.Such as exist
In step 808, processor continues left or right side, until searching out the spaced walls of desired number or cannot search out other marks
Will or spaced walls.
For example, referring to Fig. 7 D, spaced walls 718 are initially can detect.Processor continues left side, until detecting next spaced walls
716.In various embodiments, search is based on desired wall bulkhead width.Then, processor can search for 718 right side of spaced walls
Next spaced walls, spaced walls 720.Between the process can proceed with the spaced walls until searching out desired number or cannot find
Next door.
Fig. 9 shows the 2x4 subarray image sections of substrate.For example, by the smaller ones of check image, inclination can be made
The influence and optical distortion of substrate minimize.As described above, in general, the image of the central area of substrate is the figure of better quality
Picture.Therefore, the 2x4 subarrays image section in Fig. 9 can be obtained from the central area of substrate image.
Figure 10 A show the row projection 1000 of the 2x4 subarray image sections of Fig. 7.With reference to Fig. 7 A- Fig. 7 D, thrown with above-mentioned row
Shadow example is similar, can calculate base portion and remove base portion from row projection 1000, to remove unwanted and may be unfavorable number
According to.Figure 10 B show the row projection 1000 that base portion is removed.
In addition, as illustrated in figure 10 c, with similar manner as described above, it can detect row spaced walls.Here, divided by finding
Five spaced walls 1006,1008,1010,1012 and 1014 of ionic arrays detect four subarrays.
Reference point can be on the image determined in processor after row projection and row projection determine spaced walls grid.
According to each embodiment, can determined reference point be each substrate center.Then determined reference point can pass through processing
Device is by subsequent algorithm or calculates use.In other embodiments, the center of substrate can be indicated on a display screen in image
User.According to each embodiment described herein, spaced walls net center of a lattice is returned as base center.
In addition, in similar method, according to each embodiment described herein, each reflecting point is can detect (as respectively
A hole).First, drop shadow curve can be with threshold value comparison.For example, in fig. 11, drop shadow curve 1100 can with predetermined threshold value comparison,
So that the data on threshold value become the value of threshold value and the data vanishing under threshold value.This is based on Otsu threshold methods.
It should be appreciated, however, that other threshold methods can be used.
As shown in figure 12, in this way, it may be determined that the region for being each zero, so as to find each reflecting point.
Analysis is the adaptability Otsu thresholdings of the zonule based on projection, and spaced walls pass through between adjacent spaces wall
The spot hole of dose known amounts and the width at hole interval identify." pod " is also referred to as in code midpoint hole.
According to each embodiment described herein, base portion can be by the flow method shown in figure of Figure 13 from picture number
According to calculating.The example images of a substrate are shown in Figure 14.As shown in figure 14, dust granule and on the housing of substrate
Cut may include in the picture and generate background noise or undesirable data.
As described above, can be that two-dimensional surface calculates base portion, to obtain more accurately reflecting point position in various embodiments
It determines.Two-dimentional base portion is for removal due to the slowly varying dynamic back of the body caused by discrete, chemical agent transmitting crosstalk, excitation optical crosstalk
Scape.Each subarray (unit of predetermined pattern) is isolated by the border of adjacent reaction point.The part including subarray can be calculated, and
And it is used to fill the region in the part along the data sample of the segment boundary.Gap between other parts is filled, each
Part surrounds subarray, and being smoothed of base portion.Final result is used to remove base portion.According to illustrative methods, in step
In 1302, the position of subarray and then reflecting point is determined according to the above method.It should be appreciated, however, that other are implemented
Mode may include the other configurations and geometry for the substrate being analyzed in the picture, may include or may not include subarray.
After the position of subarray is determined, as described above, base portion is generated, represented with forming two-dimentional base portion.In other examples, it is sub
Array can hexagonal shape, this needs to determine in the base portions of six dimensions.
Base portion expression data for each subarray are determined and are shown in Figure 15 A.Because the spaced walls of substrate
Image data by the sample volume for determining to be included in subarray the unwanted data of data, so between subarray
Gap determine to exclude from the base portion for each subarray.Therefore, in step 1304, entire substrate base portion generation by into
One step processing, with the region between smooth subarray.That is, it is determined using for the base portion of each subarray, per height
The data in gap are interpolated between array.In some instances, interpolation can utilize linear interpolation function to implement.Figure 15 B are shown
The base portion of modification with the interpolation region between being determined positioned at each subarray base portion represents.
Referring back to method 1300, in step 1308, being smoothed of data for the whole surface that base portion represents, with into one
Step removal noise.For example, smoothing can be rectangular window, Hann windows, Kaiser-Bessel windows, Hamming windows, Gaussian
Window or Harris windows.Show that the base portion of the smoothing represents in Figure 15 C.
In step 1310, the base portion expression of image can be subtracted from original image (Figure 14), to be formed as shown in figure 16
Subtract the image of background.
In each embodiment, after the adjacent domain of all positions of reflecting point determines, fitting can be passed through
Second order polynomial subtly adjusts the position of each reflecting point to the row or column of reflecting point.The curve of order 2 may further be every
A reflecting point determines more accurately position.According to each embodiment, in this way, can make by foreign body (such as dirt and ash
Dirt) caused by optical distortion it is minimised.
Therefore, according to above, some examples of the disclosure include：
In one example, the method for providing to improve picture quality.This method includes：Receive the picture number of substrate
According to wherein image data is by making substrate imaging generation；And generate image from image data；From the background noise portions of image
It generates background to represent, wherein background parts include further handling undesirable signal message；By subtracting the back of the body from image
Scape represents that generation subtracts the image of background.
Additionally or alternatively, in above-disclosed one or more examples, substrate includes multiple region-of-interests.
Additionally or alternatively, in above-disclosed one or more examples, multiple region-of-interests are multiple reflecting points.
Additionally or alternatively, in above-disclosed one or more examples, background parts include the first background parts
With the second background parts.
Additionally or alternatively, in above-disclosed one or more examples, the first background parts are from the in image
One area determines.
Additionally or alternatively, in above-disclosed one or more examples, the second background parts are based on first back of the body
Scape part carries out interpolation from the secondth area in image, wherein the secondth area does not include region-of-interest.
In another example, the method implemented by computer of definite substrate location is provided.This method includes：By handling
Device receives the image data of substrate, and wherein image data is by generating substrate imaging；It is given birth to by processor based on image data
Into data for projection；For the known markers pattern of substrate, data for projection is assessed by processor, wherein known markers pattern
Storage is in memory；And determine the known markers pattern of substrate in image data based on the step of assessment by processor
Position.
Additionally or alternatively, in above-disclosed one or more examples, this method further includes：It is based on by processor
The center of the determined location determination substrate of known markers pattern of substrate.
Additionally or alternatively, in above-disclosed one or more examples, this method further includes：Based on data for projection
Determine base portion, wherein base portion includes further handling undesirable signal message；And processing image data, to remove base
Portion.
Additionally or alternatively, in above-disclosed one or more examples, generation data for projection includes calculating path
Integration.
Additionally or alternatively, in above-disclosed one or more examples, generation data for projection is included based on gray scale
Grade measured value calculates path integral in the columns and rows of image data.
Additionally or alternatively, in above-disclosed one or more examples, it is known that pattern include being located at base
Spaced walls between the reflecting point area at bottom.
Additionally or alternatively, in above-disclosed one or more examples, this method further includes：It is based on by processor
At least one identifier in determined location determination substrate.
Additionally or alternatively, in above-disclosed one or more examples, the step of determining identifier, includes being based on
The desired locations analysis image data of determined position and identifier in substrate, wherein desired locations are stored in memory
In.
In another example, computer readable storage medium is provided, coding has instruction, which can be held by processor
Row.The instruction includes：For receiving the instruction of the image data of substrate, wherein image data is by generating substrate imaging；
For the instruction based on image data generation data for projection；For being commented for the known markers pattern of substrate data for projection
The instruction estimated, wherein known markers pattern store in memory；And the known markers figure for determining substrate based on assessment
The instruction of position of the case in image data.
Additionally or alternatively, in above-disclosed one or more examples, which further includes：For by processor
The instruction at the center of the determined location determination substrate of known markers pattern based on substrate.
Additionally or alternatively, in above-disclosed one or more examples, which further includes：For being based on projecting
Data determine the instruction of base portion, and wherein base portion includes further handling undesirable signal message；And scheme for handling
As data to remove the instruction of base portion.
Additionally or alternatively, in above-disclosed one or more examples, generation data for projection includes calculating path
Integration.
Additionally or alternatively, in above-disclosed one or more examples, generation data for projection is included based on gray scale
Grade measured value calculates path integral in the columns and rows of image data.
Additionally or alternatively, in above-disclosed one or more examples, it is known that pattern includes being located at substrate
Reflecting point area between spaced walls.
Additionally or alternatively, in above-disclosed one or more examples, which further includes：For by processor
Instruction based at least one identifier in determined location determination substrate.
Additionally or alternatively, in above-disclosed one or more examples, determine that identifier includes being based on being determined
Position and identifier in substrate desired locations analysis image data, wherein desired locations storage in memory.
In another example, the system for visualizing multiple datagrams is provided.The system includes：Processor；And
Memory, memory coding have：For receiving the instruction of the image data of substrate, wherein image data is by being imaged substrate
And it generates；For the instruction based on image data generation data for projection；For the known markers pattern for substrate to projecting number
According to the instruction assessed, the wherein storage of known markers pattern in memory；And for having determined substrate based on assessment
Know the instruction of position of the pattern in image data.
Additionally or alternatively, in above-disclosed one or more examples, memory coding is useful for by processor
The instruction at the center of the determined location determination substrate of known markers pattern based on substrate.
Additionally or alternatively, in above-disclosed one or more examples, memory coding has：For being based on projecting
Data determine the instruction of base portion, and wherein base portion includes further handling undesirable signal message；And scheme for handling
As data to remove the instruction of base portion.
Additionally or alternatively, in above-disclosed one or more examples, memory coding is useful for by processor
Instruction based at least one identifier in determined location determination substrate.
In another example, the method for providing to improve picture quality.This method includes：For the firstth area of image
Determine the first portion of base portion, wherein base portion includes further handling undesirable signal message；The secondth area for image,
The second base segments of first portion's interpolation based on base portion, wherein the secondth area does not include region-of-interest；By combine base portion
The second portion of a part and base portion generation base portion represents；Using smooth in the first portion of base portion and the second portion of base portion
Function；And base portion expression is subtracted from image, the image of background is subtracted with generation.
Additionally or alternatively, in above-disclosed one or more examples, base portion is determined for the first area of image
It is included in the data for projection that the firstth area is assessed at least two dimensions.
Additionally or alternatively, in above-disclosed one or more examples, the firstth area based on predetermined area's pattern and
It is determined.
Although the present invention is described according to some illustrative embodiments, example and application, for this field skill
Art personnel are it is readily apparent that can carry out various modifications and change without departing from the present invention.
Claims (13)
1. determine the method implemented by computer of substrate location, including：
The image data of substrate is received by processor, wherein described image data are by generating the substrate imaging；
Described image data are based on by the processor and generate data for projection；
For the known markers pattern of the substrate, the data for projection is assessed by the processor, wherein it is described
Know pattern storage in memory；
Determine the known markers pattern of the substrate in described image data based on the step of assessment by the processor
Position；
Base portion is determined based on the data for projection, wherein by by the local minimum of polynomial curve fitting data for projection come really
Determine base portion baseline；And
Image data is handled to remove the base portion, wherein removing the base from drop shadow curve by subtracting the base portion baseline
Portion.
2. the method implemented by computer according to claim 1, further includes：
The substrate as described in the known markers pattern determined location determination of the processor based on the substrate
Center.
3. the method implemented by computer according to claim 1, wherein the step of generation data for projection includes calculating path
Integration.
4. the method implemented by computer according to claim 1, wherein the step of generation data for projection is included based on gray scale
Grade measured value calculates path integral in the columns and rows of described image data.
5. the method implemented by computer according to claim 1, wherein the known markers pattern includes being located at the base
Spaced walls between the reflecting point area at bottom.
6. the method implemented by computer according to claim 1, further includes：
At least one identifier as described in the processor based on the determined location determination in substrate.
7. the method implemented by computer according to claim 6, wherein it is determined that the step of at least one identifier wraps
It includes the desired locations based on the determined position and at least one identifier on the substrate and analyzes described image
Data, wherein the desired locations are stored in the memory.
8. a kind of system for visualizing multiple datagrams, including：
Processor；And
Memory, the memory coding have：
For receiving the instruction of the image data of substrate, wherein described image data are by generating the substrate imaging；
For the instruction based on described image data generation data for projection；
For the instruction assessed for the known markers pattern of the substrate the data for projection, wherein the known mark
Will pattern is stored in the memory；
For determining the instruction of position of the known markers pattern of the substrate in described image data based on assessment；
For determining the instruction of base portion based on the data for projection, wherein passing through the office by polynomial curve fitting into data for projection
Portion's minimum value determines base portion baseline；And
For handling image data to remove the instruction of the base portion, wherein by subtracting the base portion baseline come from drop shadow curve
Remove the base portion.
9. system according to claim 8, wherein memory coding is useful for being based on the base by the processor
The instruction at the center of substrate described in the determined location determination of the known markers pattern at bottom.
10. system according to claim 8, wherein memory coding is useful for being based on being determined by the processor
The location determination described at least one identifier in substrate instruction.
11. for improving the method for picture quality, including：
The first portion of base portion is determined for the firstth area of image, wherein the base portion includes further handling undesirable letter
Number information；
For the secondth area of described image, based on the second portion of base portion described in first portion's interpolation of the base portion, wherein described
Secondth area does not include region-of-interest；
It generates base portion by combining the first portion of the base portion and the second portion of the base portion and represents；
Smooth function is applied in the first portion of the base portion and the second portion of the base portion；And
The base portion is subtracted from described image to represent, the image of background is subtracted with generation.
12. wherein, it is according to the method for claim 11, that the step of the firstth area of image determines the first portion of base portion is wrapped
Include the data for projection that firstth area is assessed by calculating path integral at least two dimensions.
13. according to the method for claim 11, wherein, firstth area is determined based on predetermined area's pattern.
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| ITVA20020060A1 (en) | 2002-11-22 | 2004-05-23 | St Microelectronics Srl | METHOD OF ANALYSIS OF IMAGES DETECTED FROM A MICRO-ARRAY |
| US7648678B2 (en) | 2002-12-20 | 2010-01-19 | Dako Denmark A/S | Method and system for pretreatment of tissue slides |
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| JPWO2005052597A1 (en) | 2003-11-27 | 2007-06-21 | アイシン精機株式会社 | Biological information inspection system |
| WO2005109316A2 (en) * | 2004-05-03 | 2005-11-17 | Perkinelmer Las, Inc. | Method and apparatus for automatically segmenting a microarray image |
| US20060036373A1 (en) | 2004-08-11 | 2006-02-16 | Srinka Ghosh | Method and system for cropping an image of a multi-pack of microarrays |
| US20070116376A1 (en) | 2005-11-18 | 2007-05-24 | Kolterman James C | Image based correction for unwanted light signals in a specific region of interest |
| JP4402090B2 (en) * | 2006-09-05 | 2010-01-20 | シャープ株式会社 | Image forming apparatus, image forming method, program, and recording medium |
| AU2008323375A1 (en) | 2007-11-13 | 2009-05-22 | Medipan Gmbh | Method for end-titre determination and the evaluation thereof by means of an indirect immunofluorescence assay |
| CN101546426B (en) * | 2009-04-30 | 2011-06-22 | 上海交通大学 | Weak luminescence image processing method based on regional augmentation and regional extraction |
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